Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

M Bantscheff, S Lemeer, MM Savitski… - Analytical and bioanalytical …, 2012 - Springer
Mass-spectrometry-based proteomics is continuing to make major contributions to the
discovery of fundamental biological processes and, more recently, has also developed into …

Proteomics by mass spectrometry: approaches, advances, and applications

JR Yates, CI Ruse… - Annual review of …, 2009 - annualreviews.org
Mass spectrometry (MS) is the most comprehensive and versatile tool in large-scale
proteomics. In this review, we dissect the overall framework of the MS experiment into its key …

2016 update of the PRIDE database and its related tools

JA Vizcaíno, A Csordas, N Del-Toro… - Nucleic acids …, 2016 - academic.oup.com
Abstract The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data
repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of …

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

JA Vizcaíno, RG Côté, A Csordas… - Nucleic acids …, 2012 - academic.oup.com
Abstract The PRoteomics IDEntifications (PRIDE, http://www. ebi. ac. uk/pride) database at
the European Bioinformatics Institute is one of the most prominent data repositories of mass …

mzML—a community standard for mass spectrometry data

L Martens, M Chambers, M Sturm… - Molecular & Cellular …, 2011 - mcponline.org
Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With
the rapid advances in mass spectrometry technology and methods, it has become …

[HTML][HTML] Discovery of antimicrobial peptides in the global microbiome with machine learning

CD Santos-Júnior, MDT Torres, Y Duan, ÁR Del Río… - Cell, 2024 - cell.com
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a
machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global …

The next level of complexity: crosstalk of posttranslational modifications

AS Venne, L Kollipara, RP Zahedi - Proteomics, 2014 - Wiley Online Library
Beside gene expression and translational control, which are relatively slow, PTM of proteins
represents the major level of regulation, from very fast and reversible to slow or irreversible …

Synthetic and systems biology for microbial production of commodity chemicals

V Chubukov, A Mukhopadhyay, CJ Petzold… - NPJ systems biology …, 2016 - nature.com
The combination of synthetic and systems biology is a powerful framework to study
fundamental questions in biology and produce chemicals of immediate practical application …

Mass spectrometry in high-throughput proteomics: ready for the big time

T Nilsson, M Mann, R Aebersold, JR Yates III… - Nature …, 2010 - nature.com
Mass spectrometry in high-throughput proteomics: ready for the big time | Nature Methods Skip
to main content Thank you for visiting nature.com. You are using a browser version with limited …

The minimum information about a proteomics experiment (MIAPE)

CF Taylor, NW Paton, KS Lilley, PA Binz… - Nature …, 2007 - nature.com
Both the generation and the analysis of proteomics data are now widespread, and high-
throughput approaches are commonplace. Protocols continue to increase in complexity as …